PlantSynBio: Construction of a plant chassis as a platform for biological discoveries and innovations

为了食用、饲料或燃料而种植的植物种类繁多，生物技术有可能提高这些植物的质量、产量和可持续性。生物技术的应用包括改善营养、增强抗压能力、固碳、生产bioplastics/biomaterials/bioproducts/biofuels，和空间探索。然而，技术壁垒目前阻碍了具有复杂新功能的工厂的建设。该项目将产生一种新颖的、首个同类平台-底盘-将使具有新特性的工厂的设计和制造成为可能。这些特性包括：1)生产杀虫剂、生物材料、生物塑料和药品等高价值化学品；2)改善碳封存，以应对全球过量二氧化碳水平；3)增强可持续性，如减少对化肥或杀虫剂的需求；4)提高对干旱和温度胁迫的复原力和适应能力。为了鼓励对科学的参与，并向年轻一代传达科学可以应对全球挑战，该项目将直接让本科生参与底盘的特征描述。为了扩大科学参与者的多样性，该项目将在新兴生物技术和计算方法方面招募和培训代表性不足的群体的成员，从而帮助培养21世纪的科学学科劳动力。在21世纪，基因组学和生物技术的结合点将是开发产量、营养和市场质量更高的植物，增强对生物和非生物逆境的适应能力，增强可持续性，和/或新的表型，如封存碳或合成生物产品、生物材料和新的自然分子的能力。为了在农业中实现这第三次绿色革命，我们需要有能力设计复杂的路径和过程，以利用植物的可持续生产平台。最小细菌和酵母基因组的开发使基因组得以重写，并提高了工程微生物对生物技术的效用。先进的植物基因组工程方法和资源对于植物在生物经济中作为可持续平台的利用至关重要。在所有被子植物中，单一或组合工程复杂的代谢途径和发育过程的一个障碍是由于完整/片段基因组和基因复制而导致的基因功能的完全冗余。该项目将开发一个大规模的基因编辑平台，用于产生基因含量和冗余减少的新型植物基因，作为一个底盘(即一个平台)，快速设计具有新表型的植物，并测试与感兴趣的生物过程相关的异源基因。这个项目将是创建真正最小的植物基因组的第一阶段，这样我们就可以开始为新的自然分子和生物过程重写基因组。由于其矮小的身材、快速的生活周期和易于转化的特点，创建最小植物基因组的合理选择是拟南芥，即鼠耳芹。我们的具体目标包括一个设计阶段和两个构建-测试-学习周期，在这个阶段，我们使用最先进的多路基因编辑方法，在18个5Mb模块中删除324个蛋白质编码基因。合成致死对的存在将通过模块的配对和更高阶的杂交来测试。机器学习方法将与经验和生物信息数据一起使用，以开发和改进预测基因可有可有性的模型。该项目将包括一个垂直整合的项目，项目和机构的所有人员都参与其中，更多的本科生可以通过一门名为建立最小植物基因组以实现可持续生物经济的定制课程参加。该项目由ENG/CBET中的细胞和生化工程计划以及BIO/MCB中的系统和合成生物学计划共同支持。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

A wide range of plants are grown for food, feed or fuel, and biotechnology has the potential to improve the quality, yield, and sustainability of these plants. Biotechnology applications include improving nutrition, enhancing resilience to stress, carbon sequestration, production of bioplastics/biomaterials/bioproducts/biofuels, and space exploration. Yet, technology barriers currently prevent construction of plants with complex new features. This project will generate a novel, first-of-its-kind platform - a chassis - that will enable the design and fabrication of plants with novel properties. These properties include 1) the production of high value chemicals such as pesticides, bio-materials, bio-plastics, and pharmaceuticals, 2) improved carbon sequestration to address excess global carbon dioxide levels, 3) enhanced sustainability such as the reduced need for fertilizer or insecticides and 4) improved resiliency and adaptation to drought and temperature stress. To encourage participation in science and to convey to a younger generation that science can address global challenges, this project will directly engage undergraduates in the characterization of the chassis. To broaden the diversity of participants in science, this project will recruit and train members of under-represented groups in emerging biotechnology and computational methods, thereby aiding development of a 21st century workforce in scientific disciplines. In the 21st century, the nexus of genomics and biotechnology will be the development of plants with improved yield, nutrition, and market quality, enhanced resilience to biotic and abiotic stressors, increased sustainability, and/or novel phenotypes such as the ability to sequester carbon or synthesize bio-products, biomaterials, and new-to-nature molecules. To achieve this ‘Third Green Revolution’ in agriculture, we need the ability to engineer complex pathways and processes to harness the sustainable production platform of plants. Development of minimal bacterial and yeast genomes have permitted the rewriting of genomes and enhanced the utility of engineered microbes for biotechnology. Advancing plant genome engineering methods and resources are essential for plants to be utilized as sustainable platforms in the bioeconomy. One barrier to either singly or combinatorial engineering complex metabolic pathways and developmental processes is the sheer redundancy of gene function due to whole/segmental genome and gene duplication in all angiosperms. This project will develop a gene editing platform at scale that will be used to generate novel plant genotypes with reduced gene content and redundancy, which can serve as chassis (i.e., a platform) to rapidly engineer plants with new phenotypes and test heterologous genes relevant to biological processes of interest. This project will be the first phase in creating a true minimal plant genome, such that we can begin to rewrite the genome for new-to-nature molecules and biological processes. Due to its small stature, rapid life cycle, and amenability to transformation, the logical choice for creating a minimal plant genome is Arabidopsis thaliana, the mouse-ear cress. Our specific aims include a design phase and two cycles of build-test-learn in which we target 324 protein-coding genes for deletion across 18 5 Mb modules that span the Arabidopsis genome using state-of-the-art multiplexed gene editing approaches. The presence of synthetic lethal pairs will be tested through pairwise and higher order crosses of the modules. Machine learning approaches will be used with empirical and bioinformatic data to develop and improve models that predict gene dispensability. This project will include a Vertically Integrated Project in which all personnel are engaged across the project and institutions and in which a larger number of undergraduates can participate via a custom course entitled Building a Minimal Plant Genome to Enable a Sustainable Bioeconomy. This project will engage under-represented groups to advance participation in STEM disciplines relevant for the 21st century.This project is jointly supported by the Cellular and Biochemical Engineering Program in ENG/CBET, and the Systems and Synthetic Biology Program in BIO/MCB.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.